I see, that's new to me. That being said, why exactly is it different than a samurai equipped with spirit, and presumably union monsters in general?

It is similar to how you can't destroy a Six Samurai monster on the field (the originals) instead of another if all of them would be destroyed. You can't tribute/destroy one card that will be destroyed in order to save another in the same situation. In the case of Mecha Phantoms you don't tribute anything, you apply their continuous effect, which prevent them from being destroyed.